{ "_id": "6ae77272818c9e3ef6dbc2c7", "Package": "randRotation", "Title": "Random Rotation Methods for High Dimensional Data with Batch\nStructure", "Version": "1.25.0", "Authors@R": "person(given = \"Peter\",\nfamily = \"Hettegger\",\nrole = c(\"aut\", \"cre\"),\nemail = \"p.hettegger@gmail.com\",\ncomment = c(ORCID = \"0000-0001-8557-588X\"))", "Description": "A collection of methods for performing random rotations on\nhigh-dimensional, normally distributed data (e.g. microarray or\nRNA-seq data) with batch structure. The random rotation\napproach allows exact testing of dependent test statistics with\nlinear models following arbitrary batch effect correction\nmethods.", "License": "GPL-3", "biocViews": "Software, Sequencing, BatchEffect, BiomedicalInformatics,\nRNASeq, Preprocessing, Microarray, DifferentialExpression,\nGeneExpression, Genetics, MicroRNAArray, Normalization,\nStatisticalMethod", "Encoding": "UTF-8", "RdMacros": "Rdpack", "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr", "URL": "https://github.com/phettegger/randRotation", "BugReports": "https://github.com/phettegger/randRotation/issues", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:52:30 UTC", "RemoteUrl": "https://github.com/bioc/randRotation", "RemoteRef": "HEAD", "RemoteSha": "6f4dc85f9f8320e82c3f36757a2826533d43b4cb", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-01 14:14:31 UTC", "User": "root" }, "Author": "Peter Hettegger [aut, cre] (ORCID:\n)", "Maintainer": "Peter Hettegger ", "_user": "bioc", "_type": "src", "_file": "randRotation_1.25.0.tar.gz", "_fileid": "https://r2.ropensci.org/580226342771c80753cdfcf2735943aeb229a3bc0d25f576f8a9c13e15197520", "_filesize": 1515956, "_sha256": "580226342771c80753cdfcf2735943aeb229a3bc0d25f576f8a9c13e15197520", "_expires": "2027-02-09T17:10:08.000Z", "_created": "2026-11-01T14:14:31.000Z", "_published": "2026-11-01T17:10:10.488Z", "_upstream": "https://github.com/bioc/randRotation", "_status": "success", "_maintainer": { "name": "Peter Hettegger", "email": "p.hettegger@gmail.com", "login": "phettegger", "description": "", "uuid": 22321986, "orcid": "0000-0001-8557-588X" }, "_jobs": [ { "job": 124873752599, "time": 141, "config": "bioc-checks", "r": "4.6.2", "check": "WARNING", "artifact": "13087538430" }, { "job": 124873752476, "time": 231, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "13087583704" }, { "job": 124873752513, "time": 208, "config": "linux-release-x86_64", "r": "4.6.2", "check": "ERROR", "artifact": "13088125249" }, { "job": 124873752575, "time": 148, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "13092678404" }, { "job": 124873752559, "time": 210, "config": "macos-release-arm64", "r": "4.6.2", "check": "ERROR", "artifact": "13092991350" }, { "job": 124865634257, "time": 299, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13086747428" }, { "job": 124873752532, "time": 106, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13087462320" }, { "job": 124873752521, "time": 122, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "13087490982" }, { "job": 124873752515, "time": 137, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "13087330700" }, { "job": 124873752695, "time": 126, "config": "windows-release-x86_64", "r": "4.6.2", "check": "ERROR", "artifact": "13087416128" } ], "_bioccheck": { "error": 0, "warning": 2, "note": 9 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41310516063", "_commit": { "id": "6f4dc85f9f8320e82c3f36757a2826533d43b4cb", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380750 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "methods", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "Rdpack", "version": ">= 0.7", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocParallel", "role": "Suggests" }, { "package": "lme4", "role": "Suggests" }, { "package": "nlme", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "testthat", "version": ">= 2.1.0", "role": "Suggests" }, { "package": "limma", "role": "Suggests" }, { "package": "sva", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.25.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.23.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "software", "sequencing", "batcheffect", "biomedicalinformatics", "rnaseq", "preprocessing", "microarray", "differentialexpression", "geneexpression", "genetics", "micrornaarray", "normalization", "statisticalmethod" ], "_stars": 0, "_contributors": [ { "user": "phettegger", "count": 50, "uuid": 22321986 }, { "user": "nturaga", "count": 10, "uuid": 2746443 }, { "user": "jwokaty", "count": 2, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 482, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 331, "source": "https://www.bioconductor.org/packages/stats/bioc/randRotation" }, "_devurl": "https://github.com/phettegger/randrotation", "_searchresults": 7, "_abi": { "exports": [ { "key": "randRotation::generic:initBatchRandrot", "hash": "8a6b3bfce07a3c78" }, { "key": "randRotation::generic:initRandrot", "hash": "31418626b354e095" }, { "key": "randRotation::generic:randrot", "hash": "5f367e7763b7349d" }, { "key": "randRotation::initBatchRandrot", "hash": "7d118d89cc57ce92" }, { "key": "randRotation::initRandrot", "hash": "87bbe7a2b24df2a1" }, { "key": "randRotation::initRandrotW", "hash": "4ff546c6d1e5d1be" }, { "key": "randRotation::rotateStat", "hash": "f371a8f61750357b" } ], "imports": [] }, "_rbuild": "4.6.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/randRotation.html" ], "_homeurl": "https://github.com/phettegger/randrotation", "_realowner": "bioc", "_cranurl": false, "_exports": [ "contrastModel", "initBatchRandrot", "initRandrot", "pFdr", "qqunif", "randorth", "randpermut", "randrot", "rotateStat", "show", "weights", "X_decomp" ], "_help": [ { "page": "randRotation-package", "title": "randRotation: Random Rotation Methods for High Dimensional Data with Batch Structure", "topics": [ "randRotation-package", "randRotation" ] }, { "page": "contrastModel", "title": "Create transformed model matrix for contrast rotation", "topics": [ "contrastModel" ] }, { "page": "dim", "title": "Dimensions of an Object", "topics": [ "dim,initBatchRandrot-method", "dim,initRandrot-method" ] }, { "page": "dimnames", "title": "Dimnames of an Object", "topics": [ "dimnames,initBatchRandrot-method", "dimnames,initRandrot-method" ] }, { "page": "initBatchRandrot-class", "title": "Initialised random rotation batch object", "topics": [ "initBatchRandrot-class" ] }, { "page": "initRandrot", "title": "Initialisation of a random rotation Object", "topics": [ "initBatchRandrot", "initBatchRandrot,list-method", "initRandrot", "initRandrot,list-method" ] }, { "page": "initRandrot-class", "title": "Initialised random rotation class", "topics": [ "initRandrot-class", "initRandrotW-class" ] }, { "page": "pFdr", "title": "Calculate resampling based p-values and FDRs", "topics": [ "pFdr" ] }, { "page": "qqunif", "title": "Quantile-Quantile plot of data sample against uniform theoretical quantiles", "topics": [ "qqunif" ] }, { "page": "randorth", "title": "Random orthogonal matrix", "topics": [ "randorth" ] }, { "page": "randpermut", "title": "Generate random permutation matrix for n samples", "topics": [ "randpermut" ] }, { "page": "randrot", "title": "Random rotation of initialised object", "topics": [ "randrot", "randrot,initBatchRandrot-method", "randrot,initRandrot-method", "randrot,initRandrotW-method" ] }, { "page": "randRotation-defunct", "title": "Defunct functions in package 'randRotation'", "topics": [ "df_estimate" ] }, { "page": "rotateStat", "title": "Generate data rotations and calculate statistics on it", "topics": [ "rotateStat" ] }, { "page": "rotateStat-class", "title": "Rotated object containing rotated and non-rotated statistics", "topics": [ "rotateStat-class" ] }, { "page": "show", "title": "Show an Object", "topics": [ "show,initBatchRandrot-method", "show,initRandrot-method", "show,rotateStat-method" ] }, { "page": "weights", "title": "Extract model weights", "topics": [ "weights,initBatchRandrot-method", "weights,initRandrot-method" ] }, { "page": "X_decomp", "title": "Decomposition of the design matrix for random rotation generation", "topics": [ "X_decomp" ] } ], "_rundeps": [ "rbibutils", "Rdpack" ], "_vignettes": [ { "source": "randRotationIntro.Rmd", "filename": "randRotationIntro.html", "title": "Random Rotation Package Introduction", "author": "Peter Hettegger", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Sample dataset", "Quick start - linear models with batch effect correction", "Basic principle of random rotation methods", "Batch effect correction with subsequent linear model analysis", "Skewed null distribution of p values", "Unskewed p-values by random rotation", "Resampling based FDR", "Contrasts", "How many rotations ?", "Correlation matrices with non-block design", "Batch effect correction with linear mixed models", "Sample dataset", "Estimation of cormat", "Random rotation", "Session info", "References" ], "created": "2020-01-03 11:20:22", "modified": "2021-02-09 09:12:13", "commits": 20 } ], "_score": 3.6020599913279625, "_indexed": true, "_nocasepkg": "randrotation", "_universes": [ "bioc", "phettegger" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.25.0", "date": "2026-11-01T14:36:05.000Z", "distro": "resolute", "commit": "6f4dc85f9f8320e82c3f36757a2826533d43b4cb", "fileid": "https://r2.ropensci.org/510ab837fba34821e510733ce88cc75725b5ecb76744345f33d7c42aabc68ca3", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310516063" }, { "r": "4.6.2", "os": "linux", "version": "1.25.0", "date": "2026-11-01T14:35:36.000Z", "distro": "resolute", "commit": "6f4dc85f9f8320e82c3f36757a2826533d43b4cb", "fileid": "https://r2.ropensci.org/88a35fc6f70f6bc870b3d76de47f8b16f4df24c37375816d136c4fd56e4f06c4", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310516063" }, { "r": "4.5.3", "os": "mac", "version": "1.25.0", "date": "2026-11-01T17:07:49.000Z", "commit": "6f4dc85f9f8320e82c3f36757a2826533d43b4cb", "fileid": "https://r2.ropensci.org/3da207de124e04d62db47cc5e1625a2f045c5399318a16b57833c48cc2e85002", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310516063" }, { "r": "4.6.2", "os": "mac", "version": "1.25.0", "date": "2026-11-01T17:09:15.000Z", "commit": "6f4dc85f9f8320e82c3f36757a2826533d43b4cb", "fileid": "https://r2.ropensci.org/b0d9d7d7ca3efbff5429cd23d174419f9d0037850078d281ccb411809e511ea0", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310516063" }, { "r": "4.6.0", "os": "wasm", "version": "1.25.0", "date": "2026-11-01T14:34:30.000Z", "commit": "6f4dc85f9f8320e82c3f36757a2826533d43b4cb", "fileid": "https://r2.ropensci.org/eb7f3b9cdcffc4db32045e0c28a8682a727f31618133c1dd79aaef26cc34fa8c", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310516063" }, { "r": "4.7.0", "os": "win", "version": "1.25.0", "date": "2026-11-01T14:16:41.000Z", "commit": "6f4dc85f9f8320e82c3f36757a2826533d43b4cb", "fileid": "https://r2.ropensci.org/d9b98a68db20a2a8ec8e13bef2ed7bea4dd87f8d87620fbec6f6cc75b598e56e", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310516063" }, { "r": "4.5.3", "os": "win", "version": "1.25.0", "date": "2026-11-01T14:17:01.000Z", "commit": "6f4dc85f9f8320e82c3f36757a2826533d43b4cb", "fileid": "https://r2.ropensci.org/66b96e043a7d0fad69691fd3d6fe2e0d2a922d0a50237ca8f9bc524e4f8c6b07", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310516063" }, { "r": "4.6.2", "os": "win", "version": "1.25.0", "date": "2026-11-01T14:16:46.000Z", "commit": "6f4dc85f9f8320e82c3f36757a2826533d43b4cb", "fileid": "https://r2.ropensci.org/476e0a8ca6c98ebafa0631719f4328fab7dc1041ef11519135f86b8661eac664", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310516063" } ] }